VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code. However, it still lacks a graphical user interface (GUI) for molecular manipulations when doing some modeling tasks.

A recent publication DOI describes work using the Tcl/Tk toolkit to develop a user-friendly GUI for VMD, named Molcontroller.

All the scripts and installation instructions are available https://github.com/ChenchenWu-hub/Molcontroller.